def annotateFile(art, file):
# example
pmid = art.pmid
if art.pmid == "" or not int(pmid) in pmidToGenes:
logging.debug("No pmid for article %s" % art.articleId)
raise StopIteration
genes = pmidToGenes[int(art.pmid)].split(",")
genes = [int(x) for x in genes]
mutations = seth.findMutations(file.content)
for gene in genes:
potentialSNPs = dbSNP.getSNP(int(gene))
features = UniprotFeature.getFeatures(gene)
for mut in mutations:
print("mutation found: ", str(mut))
start = mut.getStart()
end = mut.getEnd()
mut.normalizeSNP(potentialSNPs, features, False)
normalized = mut.getNormalized()
for snp in normalized:
wtRes = mut.getWtResidue()
mutRes = mut.getMutResidue()
pos = mut.getPosition()
text = mut.getText()
rsId = snp.getRsID()
yield [
start, end,
str(gene), wtRes, pos, mutRes, "rs" + str(rsId), text
]
def annotateFile(art, file):
# example
pmid = art.pmid
if art.pmid=="" or not int(pmid) in pmidToGenes:
logging.debug("No pmid for article %s" % art.articleId)
raise StopIteration
genes = pmidToGenes[int(art.pmid)].split(",")
genes = [int(x) for x in genes]
mutations = seth.findMutations(file.content)
for gene in genes:
potentialSNPs = dbSNP.getSNP(int(gene))
features = UniprotFeature.getFeatures(gene);
for mut in mutations:
print "mutation found: ", str(mut)
start = mut.getStart()
end = mut.getEnd()
mut.normalizeSNP(potentialSNPs, features, False)
normalized = mut.getNormalized()
for snp in normalized:
wtRes = mut.getWtResidue()
mutRes = mut.getMutResidue()
pos = mut.getPosition()
text = mut.getText()
rsId = snp.getRsID()
yield [start, end, str(gene), wtRes, pos, mutRes, "rs"+str(rsId), text]
def test():
gene = 1312
potentialSNPs = dbSNP.getSNP(gene);
features = UniprotFeature.getFeatures(gene);
mutations = seth.findMutations("p.A123T and Val158Met")
for mut in mutations:
start, end = mut.getStart(), mut.getEnd()
wtRes, mutRes = mut.getWtResidue(), mut.getMutResidue()
pos, text = mut.getPosition(), mut.getText()
mut.normalizeSNP(potentialSNPs, features, False)
normalized = mut.getNormalized()
for snp in normalized:
rsId = snp.getRsID()
print ",".join([start, end, wtRes, mutRes, pos, "rs"+str(rsId), text])
def test():
gene = 1312
potentialSNPs = dbSNP.getSNP(gene)
features = UniprotFeature.getFeatures(gene)
mutations = seth.findMutations("p.A123T and Val158Met")
for mut in mutations:
start, end = mut.getStart(), mut.getEnd()
wtRes, mutRes = mut.getWtResidue(), mut.getMutResidue()
pos, text = mut.getPosition(), mut.getText()
mut.normalizeSNP(potentialSNPs, features, False)
normalized = mut.getNormalized()
for snp in normalized:
rsId = snp.getRsID()
print(",".join(
[start, end, wtRes, mutRes, pos, "rs" + str(rsId), text]))
